Strange line of argument, this. The reason doctors are worried about "superbugs" isn't because antibiotics have somehow made them tougher or more virulent. They haven't - they're still pretty much the same bugs, just no longer responsive to antibiotics. In other words, doctors are worried about going back to the bad old days when an infected wound was almost invariably fatal.
Similar story with vaccines. If a virus evolves to evade a particular vaccine, there's no reason to expect that somehow makes it stronger. If anything, on average it would make it weaker - vaccines are usually designed to target relatively invariant sites, which are invariant for a reason: the virus needs them to be that way in order to function optimally. So mutations that evade the immune system will often come at the cost of some reduction in the virus' efficiency. And if a new, strong strain does emerge, well, we just sequence its genome and work out what to add to a new vaccine mix. Actually much, much easier than the antibiotic issue.
